8ynp | pdb_00008ynp
RNA duplex containing Methylformamide
Structural highlights
Publication Abstract from PubMedIn this study, we report the synthesis of 2'-formamidonucleoside phosphoramidite derivatives and their incorporation into siRNA strands to reduce seed-based off-target effects of small interfering RNAs (siRNAs). Formamido derivatives of all four nucleosides (A, G, C and U) were synthesized in 5-11 steps from commercial compounds. Introducing these derivatives into double-stranded RNA slightly reduced its thermodynamic stability, but X-ray crystallography and CD spectrum analysis confirmed that the RNA maintained its natural A-form structure. Although the introduction of the 2'-formamidonucleoside derivative at the 2nd position in the guide strand of the siRNA led to a slight decrease in the on-target RNAi activity, the siRNAs with different sequences incorporating 2'-formamidonucleoside with four kinds of nucleobases into any position other than 2nd position in the seed region revealed a significant suppression of off-target activity while maintaining on-target RNAi activity. This indicates that 2'-formamidonucleosides represent a promising approach for mitigating off-target effects in siRNA therapeutics. Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs.,Nomura K, An S, Kobayashi Y, Kondo J, Shi T, Murase H, Nakamoto K, Kimura Y, Abe N, Ui-Tei K, Abe H Nucleic Acids Res. 2024 Oct 14;52(18):10754-10774. doi: 10.1093/nar/gkae741. PMID:39231537[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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